I have the Prometheus System extruders which are similar in principle to the SeeMeCNC Y Coupler. I figured maybe I should update from my old but working .91 firmware (fine with the dual extruders) on the Rostock Max V2 to the later SeeMeCNC version of 0.92.4.

So It now has tweaks in it for dual extruders (your Y-coupler junction like the Pro System), great. However after uploading, testing extrusion in Mattercontrol:

- EXT0 extrudes fine, +10mm extruders 10mm on EXT0- EXT1 however.. trying to extruder 10mm from EXT1 makes EXT0 do some purge type behaviour, then rapidly shoots a huge amount of filament out of EXT1, which then retracts, then extrudes a bit then EXT0 comes online again and starts pushing and pulling filament too!!?

What is this behavior about? Can I use 2 extruders without this auto-retract scripting (and supply my own as with the Prometheus System)?

Correct! The firmware is setup to automatically retract the current extruder far enough to clear the Y and then push the new extruder forward all the way to the nozzle. It's hard coded in the firmware, but can be changed if you still want to run that firmware. Take a look at lines 149, 150, 182, and 183 in Configuration.h, that's the GCode it runs when it's changing extruders. You can set it to anything you want and you've got decent odds it'll work for you.